delangel cb1e8ad43a Temp bug fix for indel genotyper: if there are two or more variant contexts at a site, just choose the first one containing an indel and genotype that. There might be cases where IGv2 emits 2 indel variant contexts in at the same ref location which made us fail there. A better solution will be to form underlying haplotypes supported by reads and compute likelihoods of that. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4667 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-14 00:21:54 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Temp bug fix for indel genotyper: if there are two or more variant contexts at a site, just choose the first one containing an indel and genotype that. There might be cases where IGv2 emits 2 indel variant contexts in at the same ref location which made us fail there. A better solution will be to form underlying haplotypes supported by reads and compute likelihoods of that.	2010-11-14 00:21:54 +00:00
test	New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s	2010-11-13 16:19:56 +00:00